D-I-TASSER A6NHG4

D-I-TASSER results for A6NHG4

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: A6NHG4
Protein Name: D-dopachrome decarboxylase-like protein
Gene Name: DDTL

Input Sequence in FASTA format

>A6NHG4 (134 residues)
MPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQL
SISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRFPTVLSTSPAAHGGPRCPGEIIEGK
KSCLNEEALFIYFI

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	A6NHG4-D1	1-134	134		MPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRFPTVLSTSPAAHGGPRCPGEIIEGKKSCLNEEALFIYFI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7715

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6lkvF	0.83	1.65	0.177	0.918	model1_6lkvF.pdb.gz
2	2os5A	0.82	1.32	0.288	0.881	model1_2os5A.pdb.gz
3	1uizA	0.81	1.18	0.304	0.858	model1_1uizA.pdb.gz
4	1gczA	0.80	1.37	0.322	0.866	model1_1gczA.pdb.gz
5	1dptA	0.80	1.46	0.821	0.873	model1_1dptA.pdb.gz
6	1hfoA	0.78	1.29	0.292	0.843	model1_1hfoA.pdb.gz
7	3gacC	0.78	1.79	0.207	0.866	model1_3gacC.pdb.gz
8	2xczA	0.78	1.54	0.254	0.851	model1_2xczA.pdb.gz
9	4dh4A	0.75	1.75	0.239	0.843	model1_4dh4A.pdb.gz
10	3fwuA	0.75	1.77	0.250	0.836	model1_3fwuA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	0.87	catalytic activity
GO:0016860	0.81	intramolecular oxidoreductase activity
GO:0004167	0.78	dopachrome isomerase activity
GO:0005102	0.59	receptor binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

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[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.85	single-organism process
GO:0065007	0.84	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0009987	0.84	cellular process
GO:0050794	0.80	regulation of cellular process
GO:0008152	0.74	metabolic process
GO:0050896	0.70	response to stimulus
GO:0048523	0.70	negative regulation of cellular process
GO:0044237	0.69	cellular metabolic process
GO:0043066	0.69	negative regulation of apoptotic process
GO:0006950	0.69	response to stress
GO:0071704	0.66	organic substance metabolic process
GO:0044763	0.63	single-organism cellular process
GO:0048518	0.62	positive regulation of biological process
GO:0044281	0.61	small molecule metabolic process
GO:0051049	0.60	regulation of transport
GO:0002376	0.60	immune system process
GO:0048584	0.59	positive regulation of response to stimulus
GO:0048522	0.59	positive regulation of cellular process
GO:0044238	0.59	primary metabolic process
GO:0006952	0.59	defense response
GO:0002684	0.59	positive regulation of immune system process
GO:0080134	0.58	regulation of response to stress
GO:0080090	0.58	regulation of primary metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0006954	0.58	inflammatory response
GO:0051239	0.57	regulation of multicellular organismal process
GO:0050793	0.57	regulation of developmental process
GO:0080135	0.56	regulation of cellular response to stress
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0051050	0.56	positive regulation of transport
GO:0042327	0.56	positive regulation of phosphorylation
GO:1901576	0.55	organic substance biosynthetic process
GO:0065008	0.55	regulation of biological quality
GO:0044249	0.54	cellular biosynthetic process
GO:0050778	0.53	positive regulation of immune response
GO:0019752	0.53	carboxylic acid metabolic process
GO:0010468	0.53	regulation of gene expression
GO:1902531	0.52	regulation of intracellular signal transduction
GO:0051251	0.52	positive regulation of lymphocyte activation
GO:0032787	0.52	monocarboxylic acid metabolic process
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0016043	0.52	cellular component organization
GO:0006955	0.52	immune response
GO:0045087	0.51	innate immune response
GO:0044283	0.51	small molecule biosynthetic process
GO:0043516	0.51	regulation of DNA damage response, signal transduction by p53 class mediator
GO:0022607	0.51	cellular component assembly
GO:0010739	0.51	positive regulation of protein kinase A signaling
GO:0010629	0.51	negative regulation of gene expression
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0001819	0.51	positive regulation of cytokine production
GO:1902166	0.50	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0090344	0.50	negative regulation of cell aging
GO:0071157	0.50	negative regulation of cell cycle arrest
GO:0070374	0.50	positive regulation of ERK1 and ERK2 cascade
GO:0070207	0.50	protein homotrimerization
GO:0050731	0.50	positive regulation of peptidyl-tyrosine phosphorylation
GO:0050715	0.50	positive regulation of cytokine secretion
GO:0048146	0.50	positive regulation of fibroblast proliferation
GO:0044767	0.50	single-organism developmental process
GO:0043518	0.50	negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0043270	0.50	positive regulation of ion transport
GO:0033138	0.50	positive regulation of peptidyl-serine phosphorylation
GO:0032103	0.50	positive regulation of response to external stimulus
GO:0030890	0.50	positive regulation of B cell proliferation
GO:0001516	0.50	prostaglandin biosynthetic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.93	cell part
GO:0043227	0.88	membrane-bounded organelle
GO:0044424	0.82	intracellular part
GO:0044421	0.77	extracellular region part
GO:0070062	0.70	extracellular exosome

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.521	1dptB	0.799	1.46	0.821	0.873	4.1.1.84	3,5,25,29,31,33,35,39,41,61,63,67,80
2	0.181	1hfoA	0.784	1.29	0.292	0.843	5.3.3.12 5.3.2.1	82,89
3	0.166	1fimA	0.710	1.40	0.324	0.761	5.3.2.1	57
4	0.060	2j5nB	0.472	4.60	0.087	0.798	1.5.1.12	24,26
5	0.060	1t90D	0.486	4.67	0.079	0.813	1.2.1.27	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.64	1gczB	0.794	1.25	0.333	0.851	1.14	YZ9	complex1.pdb.gz	33,37,63,64,65,108,117
2	0.47	3l5tA	0.792	1.28	0.333	0.851	0.89	956	complex2.pdb.gz	2,3,34,63,64,65,108,110,117
3	0.46	3jsgB	0.793	1.27	0.333	0.851	1.07	0IN	complex3.pdb.gz	2,3,64,65,108
4	0.43	1ljtB	0.796	1.22	0.333	0.851	0.94	HDI	complex4.pdb.gz	2,3,33,63,64,65,103
5	0.36	3kanB	0.800	1.46	0.821	0.873	0.98	RW1	complex5.pdb.gz	2,3,34,37,39
6	0.31	3l5sA	0.792	1.27	0.333	0.851	1.01	88X	complex6.pdb.gz	32,37,65,110

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.